ajrange.c

Section: Range Constructors

Functions:

ajRangeNewI	Default constructor for AJAX range objects.
ajRangeNewFilename	Load a range object from a file
ajRangeNewFilenameLimits	Load a range object from a file
ajRangeNewRange	Copy constructor for AJAX range objects.
ajRangeNewString	Create a range object from a string
ajRangeNewStringLimits	Create a range object from a string

Function ajRangeNewI

Prototype

AjPRange ajRangeNewI (
      ajuint n
);

Type	Name	Read/Write	Description
ajuint	n	Input	number of ranges
AjPRange		RETURN	Pointer to a range object

From EMBOSS 1.0.0

Function ajRangeNewFilename

Prototype

AjPRange ajRangeNewFilename (
      const AjPStr name
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	range file name
AjPRange		RETURN	range object

From EMBOSS 6.2.0

Function ajRangeNewFilenameLimits

Prototype

AjPRange ajRangeNewFilenameLimits (
      const AjPStr name,
      ajuint imin,
      ajuint imax,
      ajuint minsize,
      ajuint size
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	range file name
ajuint	imin	Input	Minimum value
ajuint	imax	Input	Maximum value
ajuint	minsize	Input	Minimum number of values
ajuint	size	Input	Required number of values, zero for unlimited
AjPRange		RETURN	range object

From EMBOSS 6.2.0

Function ajRangeNewRange

Prototype

AjPRange ajRangeNewRange (
      const AjPRange src
);

Type	Name	Read/Write	Description
const AjPRange	src	Input	Source range
AjPRange		RETURN	Pointer to a range object

From EMBOSS 6.2.0

Function ajRangeNewString

Prototype

AjPRange ajRangeNewString (
      const AjPStr str
);

Type	Name	Read/Write	Description
const AjPStr	str	Input	range string
AjPRange		RETURN	range object

From EMBOSS 6.2.0

Function ajRangeNewStringLimits

Prototype

AjPRange ajRangeNewStringLimits (
      const AjPStr str,
      ajuint imin,
      ajuint imax,
      ajuint minsize,
      ajuint size
);

Type	Name	Read/Write	Description
const AjPStr	str	Input	range string
ajuint	imin	Input	Minimum value
ajuint	imax	Input	Maximum value
ajuint	minsize	Input	Minimum number of values
ajuint	size	Input	Required number of values, zero for unlimited
AjPRange		RETURN	range object

From EMBOSS 6.2.0

Section: Range Destructors

Functions:

ajRangeDel

Default destructor for AJAX range objects.

Function ajRangeDel

Prototype

void ajRangeDel (
      AjPRange* thys
);

Type	Name	Read/Write	Description
AjPRange*	thys	Delete	range structure
void		RETURN

From EMBOSS 1.0.0

Section: Range Functions

Functions:

ajRangeGetSize	Return the number of ranges in a range object
ajRangeElementGetText	Return (as parameters) text value of a range element
ajRangeElementGetValues	Return (as parameters) start and end values in a range
ajRangeElementSet	Set the values of a start and end in a (pre-existing) range element
ajRangeSetOffset	Sets the range values offset relative to the Begin value.
ajRangeSeqExtractList	Extract the range from a sequence and place the resulting text in a list of strings.
ajRangeSeqExtract	Extract the range from a sequence (Remove regions not in the range(s)) N.B. the resulting sequence will be regions of the original concatenated in the order specified in the set of ranges. If these are not in ascending order, the resulting sequence will not be in position order either.
ajRangeSeqExtractPep	Extract the range from a sequence (Remove regions not in the range(s)) and translate to protein.
ajRangeSeqStuff	The opposite of ajRangeSeqExtract() Stuff space characters into a string to pad out to the range.
ajRangeSeqStuffPep	The opposite of ajRangeSeqExtractPep() Stuff space characters into a translated string to pad out to the range.
ajRangeSeqMask	Mask the range in a String
ajRangeSeqToLower	Change the range in a String to lower-case
ajRangeStrExtractList	Extract the range from a String and place the resulting text in a list of strings.
ajRangeStrExtract	Extract the range from a String (Remove regions not in the range(s))
ajRangeStrStuff	The opposite of ajRangeStrExtract() Stuff space characters into a string to pad out to the range.
ajRangeStrMask	Mask the positions defined by a range in a string
ajRangeStrToLower	Change positions defined by the range in a string to lower-case
ajRangeElementTypeOverlap	Detect an overlap of a single range element to a region of a sequence
ajRangeCountOverlaps	Detect overlaps of a set of ranges to a region of a sequence
ajRangeIsOrdered	Tests to see if the set of ranges are in ascending non-overlapping order
ajRangeIsWhole	Test whether the default range is used for a sequence

Function ajRangeGetSize

Prototype

ajuint ajRangeGetSize (
      const AjPRange thys
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
ajuint		RETURN	number of ranges

From EMBOSS 6.2.0

Function ajRangeElementGetText

Prototype

AjBool ajRangeElementGetText (
      const AjPRange thys,
      ajuint element,
      AjPStr* text
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
ajuint	element	Input	range element (0 to n-1)
AjPStr*	text	Output	text value
AjBool		RETURN	true if range exists

From EMBOSS 6.2.0

Function ajRangeElementGetValues

Prototype

AjBool ajRangeElementGetValues (
      const AjPRange thys,
      ajuint element,
      ajuint* start,
      ajuint* end
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
ajuint	element	Input	range element (0 to n-1)
ajuint*	start	Output	start value
ajuint*	end	Output	end value
AjBool		RETURN	true if range exists

From EMBOSS 6.2.0

Function ajRangeElementSet

Prototype

AjBool ajRangeElementSet (
      AjPRange thys,
      ajuint element,
      ajuint start,
      ajuint end
);

Type	Name	Read/Write	Description
AjPRange	thys	Output	range object
ajuint	element	Input	range element (0 to n-1)
ajuint	start	Input	start value
ajuint	end	Input	end value
AjBool		RETURN	true if range exists

From EMBOSS 6.2.0

Function ajRangeSetOffset

Prototype

AjBool ajRangeSetOffset (
      AjPRange thys,
      ajuint begin
);

Type	Name	Read/Write	Description
AjPRange	thys	Modify	range object
ajuint	begin	Input	begin parameter obtained from ajSeqGetBegin(seq)
AjBool		RETURN	true if region values modified

From EMBOSS 6.2.0

Function ajRangeSeqExtractList

Prototype

AjBool ajRangeSeqExtractList (
      const AjPRange thys,
      const AjPSeq seq,
      AjPList outliststr
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPSeq	seq	Input	sequence to extract from
AjPList	outliststr	Output	resulting list of strings
AjBool		RETURN	true if result is not the whole sequence

From EMBOSS 3.0.0

Function ajRangeSeqExtract

Prototype

AjBool ajRangeSeqExtract (
      const AjPRange thys,
      AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPSeq	seq	Modify	Sequence
AjBool		RETURN	true if sequence was modified

From EMBOSS 3.0.0

Function ajRangeSeqExtractPep

Prototype

AjPSeq ajRangeSeqExtractPep (
      const AjPRange thys,
      AjPSeq seq,
      const AjPTrn trntable,
      ajint frame
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPSeq	seq	Modify	Sequence
const AjPTrn	trntable	Input	Translation table
ajint	frame	Input	Reading frame 1..3 or -1..-3
AjPSeq		RETURN	Translated protein sequence

From EMBOSS 6.1.0

Function ajRangeSeqStuff

Prototype

AjBool ajRangeSeqStuff (
      const AjPRange thys,
      AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPSeq	seq	Modify	Sequence to be modified
AjBool		RETURN	true if sequence was modified

From EMBOSS 3.0.0

Function ajRangeSeqStuffPep

Prototype

AjBool ajRangeSeqStuffPep (
      const AjPRange thys,
      AjPSeq seq,
      ajint frame
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPSeq	seq	Modify	Sequence to be modified
ajint	frame	Input	Reading frame 1..3 or -1..-3
AjBool		RETURN	true if sequence was modified

From EMBOSS 6.1.0

Function ajRangeSeqMask

Prototype

AjBool ajRangeSeqMask (
      const AjPRange thys,
      const AjPStr maskchar,
      AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPStr	maskchar	Input	character to mask with
AjPSeq	seq	Modify	sequence to be masked
AjBool		RETURN	true if string modified

From EMBOSS 3.0.0

Function ajRangeSeqToLower

Prototype

AjBool ajRangeSeqToLower (
      const AjPRange thys,
      AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPSeq	seq	Modify	sequence to be lower-cased
AjBool		RETURN	true if sequence was modified

From EMBOSS 3.0.0

Function ajRangeStrExtractList

Prototype

AjBool ajRangeStrExtractList (
      const AjPRange thys,
      const AjPStr instr,
      AjPList outliststr
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPStr	instr	Input	string to extract from
AjPList	outliststr	Output	resulting list of strings
AjBool		RETURN	true if string modified

From EMBOSS 1.0.0

Function ajRangeStrExtract

Prototype

AjBool ajRangeStrExtract (
      const AjPRange thys,
      const AjPStr instr,
      AjPStr* outstr
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPStr	instr	Input	string to extract from
AjPStr*	outstr	Output	resulting extracted string
AjBool		RETURN	true if string modified

From EMBOSS 1.0.0

Function ajRangeStrStuff

Prototype

AjBool ajRangeStrStuff (
      const AjPRange thys,
      const AjPStr instr,
      AjPStr* outstr
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPStr	instr	Input	string to stuff
AjPStr*	outstr	Output	resulting stuffed string
AjBool		RETURN	true if string modified

From EMBOSS 1.0.0

Function ajRangeStrMask

Prototype

AjBool ajRangeStrMask (
      const AjPRange thys,
      const AjPStr maskchar,
      AjPStr* str
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPStr	maskchar	Input	character to mask with
AjPStr*	str	Output	string to be masked
AjBool		RETURN	true if string modified

From EMBOSS 1.0.0

Function ajRangeStrToLower

Prototype

AjBool ajRangeStrToLower (
      const AjPRange thys,
      AjPStr* str
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjPStr*	str	Output	string to be lower-cased
AjBool		RETURN	true if string modified

From EMBOSS 2.7.0

Function ajRangeElementTypeOverlap

Prototype

ajuint ajRangeElementTypeOverlap (
      const AjPRange thys,
      ajuint element,
      ajuint pos,
      ajuint length
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
ajuint	element	Input	range element (0 to n-1)
ajuint	pos	Input	position in sequence of start of region of sequence
ajuint	length	Input	length of region of sequence
ajuint		RETURN	0=no overlap 1=internal 2=complete 3=at left 4=at right

From EMBOSS 6.2.0

Function ajRangeCountOverlaps

Prototype

ajuint ajRangeCountOverlaps (
      const AjPRange thys,
      ajuint pos,
      ajuint length
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
ajuint	pos	Input	position in sequence of start of region of sequence
ajuint	length	Input	length of region of sequence
ajuint		RETURN	Number of ranges in range object with overlaps to the region

From EMBOSS 6.2.0

Function ajRangeIsOrdered

Prototype

AjBool ajRangeIsOrdered (
      const AjPRange thys
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
AjBool		RETURN	ajTrue if in ascending non-overlapping order

From EMBOSS 6.2.0

Function ajRangeIsWhole

Prototype

AjBool ajRangeIsWhole (
      const AjPRange thys,
      const AjPSeq s
);

Type	Name	Read/Write	Description
const AjPRange	thys	Input	range object
const AjPSeq	s	Input	sequence
AjBool		RETURN	true if default range

From EMBOSS 6.2.0